[Best practice] Upgrade custom module

We have developed/deployed a custom Package containing some custom Modules and some customisation of existing Modules. The new modules were created using Module Builder. Then the code was modified, evolved to the final version and installed on the production server.

Now we need to update some modules by adding some fields and logic to one or more of the custom Modules.

What is the best known practice to achieve this?

Change manifest.php to add custom fields, this is what I used for existing Modules, like Contacts?